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comparison abromics_galaxy_json_extractor.xml @ 0:a157d29ef11d draft default tip

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planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
author pimarin
date Mon, 15 May 2023 14:20:18 +0000
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1 <tool id="abromicsextractor" name="abromicsextractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 Result extractor to json format
4 </description>
5 <macros>
6 <import>macro.xml</import>
7 </macros>
8 <expand macro='edam'/>
9 <expand macro="requirements"/>
10 <expand macro="version_command"/>
11
12 <command detect_errors="aggressive"><![CDATA[
13
14 mkdir "abromics_extracted_folder" &&
15 #*=================================================================
16 Paramaters to add Database and tool version if available
17 =================================================================*#
18 #set $software_with_database = str("abricate,bakta,bracken,kraken2,plasmidfinder,recentrifuge").split(",")
19
20 #*======================================================
21 Loop to include some different tool in one time
22 ======================================================*#
23 #for $i, $tool in enumerate( $tool_section.tools )
24 abromics
25 "$tool.select_tool.tool_list"
26 --hid $tool.select_tool.input.hid
27 "$tool.select_tool.input"
28 --analysis_software_version "$tool.select_tool.analysis_software_version"
29 #if str($tool.select_tool.tool_list) in str($software_with_database)
30 --reference_database_version "$tool.select_tool.reference_database_version"
31 #end if
32 #if "$tool.select_tool.tool_list" == "bakta"
33 --summary_result_path "$tool.select_tool.summary_result_path"
34 --nucleotide_annotation_path "$tool.select_tool.nucleotide_annotation_path"
35 --amino_acid_annotation_path "$tool.select_tool.amino_acid_annotation_path"
36 --gff_file_path "$tool.select_tool.gff_file_path"
37 #elif "$tool.select_tool.tool_list" == "bracken"
38 --kraken_report_path "tool.select_tool.kraken_report_path"
39 --threshold "tool.select_tool.threshold"
40 --read_length "tool.select_tool.read_length"
41 --level "tool.select_tool.level"
42 #elif"$tool.select_tool.tool_list" == "integronfinder2"
43 --summary_file_path "tool.select_tool.summary_file_path"
44 #elif "$tool.select_tool.tool_list" == "isescan"
45 --orf_fna_file "tool.select_tool.orf_fna_file"
46 --orf_faa_file "tool.select_tool.orf_faa_file"
47 --is_fna_file "tool.select_tool.is_fna_file"
48 #elif "$tool.select_tool.tool_list" == "kraken2"
49 --seq_classification_file_path "tool.select_tool.seq_classification_file_path"
50 #elif "$tool.select_tool.tool_list" == "plasmidfinder"
51 --genome_hit_file_path "tool.select_tool.genome_hit_file_path"
52 --plasmid_sequence_file_path "tool.select_tool.plasmid_sequence_file_path"
53 #elif "$tool.select_tool.tool_list" == "recentrifuge"
54 --rcf_stat_file_path "tool.select_tool.rcf_stat_file_path"
55 --rcf_html_path "tool.select_tool.rcf_html_path"
56 #elif "$tool.select_tool.tool_list" == "shovill"
57 --contig_graph_path "tool.select_tool.contig_graph_path"
58 --bam_file_path "tool.select_tool.bam_file_path"
59 #elif "$tool.select_tool.tool_list" == "staramr"
60 --mlst_file_path "tool.select_tool.mlst_file_path"
61 --plasmidfinder_file_path "tool.select_tool.plasmidfinder_file_path"
62 --pointfinder_file_path "tool.select_tool.pointfinder_file_path"
63 --setting_file_path "tool.select_tool.setting_file_path"
64 #elif "$tool.select_tool.tool_list" == "tabular_file"
65 --analysis_software_name "tool.select_tool.analysis_software_name"
66 #end if
67 -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json"
68 | tee "$logfile" ;
69 #end for
70 #if $summarize == "true"
71 abromics summarize abromics_extracted_folder/* -o abromics_summary.json &&
72 rm -r abromics_extracted_folder
73 #end if
74 ]]>
75 </command>
76 <inputs>
77 <section name="tool_section" title="Available tool screen" expanded="false">
78 <repeat name="tools" title="Tools" min="1">
79 <conditional name="select_tool">
80 <param name="tool_list" type="select" label="Available tools">
81 <option value="abricate">abricate</option>
82 <option value="bakta">bakta</option>
83 <option value="bandage">bandage</option>
84 <option value="bracken">bracken</option>
85 <option value="fastp">fastp</option>
86 <option value="integronfinder2">integronfinder2</option>
87 <option value="isescan">isescan</option>
88 <option value="kraken2">kraken2</option>
89 <option value="plasmidfinder">plasmidfinder</option>
90 <option value="quast">quast</option>
91 <option value="recentrifuge">recentrifuge</option>
92 <option value="refseqmasher">refseqmasher</option>
93 <option value="shovill">shovill</option>
94 <option value="staramr">staramr</option>
95 <option value="tabular_file">tabular_generic_file</option>
96 </param>
97 <when value="abricate">
98 <param name="input" type="data" format="txt,tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/>
99 <expand macro="analysis_software_version"/>
100 <expand macro="reference_database_version"/>
101 </when>
102 <when value="bakta">
103 <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/>
104 <param argument="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/>
105 <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide file" help="Nucleotide sequence annotation file"/>
106 <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta amino acide file" help="Amino acid sequence annotation file"/>
107 <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file"/>
108 <expand macro="analysis_software_version"/>
109 <expand macro="reference_database_version"/>
110 </when>
111 <when value="bandage">
112 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/>
113 <expand macro="analysis_software_version"/>
114 </when>
115 <when value="bracken">
116 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
117 <expand macro="analysis_software_version"/>
118 <expand macro="reference_database_version"/>
119 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
120 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
121 <param argument="--read_length" type="integer" min="0" optional="true" label="Read length"/>
122 <param argument="--level" type="select" label="Taxonomic level estimation" help="Level of final abundance (from Domain to subspecies, default on species)">
123 <option value="D">Domain</option>
124 <option value="P">Phylum</option>
125 <option value="C">Class</option>
126 <option value="O">Order</option>
127 <option value="F">Family</option>
128 <option value="G">Genus</option>
129 <option value="S">Species</option>
130 <option value="S+">Subspecies</option>
131 </param>
132 </when>
133 <when value="fastp">
134 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
135 <expand macro="analysis_software_version"/>
136 </when>
137 <when value="integronfinder2">
138 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
139 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" label="Summary report" help="Summary file from integronfinder2"/>
140 <expand macro="analysis_software_version"/>
141 </when>
142 <when value="isescan">
143 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/>
144 <param argument="--orf_fna_file" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/>
145 <param argument="--orf_faa_file" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/>
146 <param argument="--is_fna_file" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/>
147 <expand macro="analysis_software_version"/>
148 </when>
149 <when value="kraken2">
150 <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/>
151 <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/>
152 <expand macro="analysis_software_version"/>
153 <expand macro="reference_database_version"/>
154 </when>
155 <when value="plasmidfinder">
156 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/>
157 <param argument="--genome_hit_file_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
158 <param argument="--plasmid_sequence_file_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
159 <expand macro="analysis_software_version"/>
160 <expand macro="reference_database_version"/>
161 </when>
162 <when value="quast">
163 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
164 <expand macro="analysis_software_version"/>
165 </when>
166 <when value="recentrifuge">
167 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/>
168 <param argument="--rcf_stat_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/>
169 <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/>
170 <expand macro="analysis_software_version"/>
171 <expand macro="reference_database_version"/>
172 </when>
173 <when value="refseqmasher">
174 <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/>
175 <expand macro="analysis_software_version"/>
176 </when>
177 <when value="shovill">
178 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/>
179 <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/>
180 <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/>
181 <expand macro="analysis_software_version"/>
182
183 </when>
184 <when value="staramr">
185 <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/>
186 <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/>
187 <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/>
188 <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/>
189 <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/>
190 <expand macro="analysis_software_version"/>
191 </when>
192 <when value="tabular_file">
193 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
194 <param argument="--analysis_software_name" type="text" multiple="false" label="Tool name" help="Tool name which generated the result file"/>
195 <expand macro="analysis_software_version"/>
196 </when>
197 </conditional>
198 </repeat>
199 </section>
200 <param argument="summarize" type="boolean" truevalue="true" falsevalue="" label="Summarize results" help="Summarize all outputs in only one file"/>
201 <param name="log" type="boolean" truevalue="true" falsevalue="" label="Add log" help="Activate/Deactivate the log"/>
202 </inputs>
203 <outputs>
204 <collection name="output_json" type="list" label="${tool.name} on ${on_string}: abromics formated json results">
205 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="abromics_extracted_folder" />
206 </collection>
207 <data name="summary_json" format="json" from_work_dir="abromics_summary.json" label="${tool.name} on ${on_string}: Summarized file">
208 <filter> summarize == True </filter>
209 </data>
210 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
211 <filter> log == True </filter>
212 </data>
213 </outputs>
214 <tests>
215 <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile -->
216 <section name="tool_section">
217 <repeat name="tools">
218 <conditional name="select_tool">
219 <param name="tool_list" value="abricate"/>
220 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
221 <param name="analysis_software_version" value="1.0"/>
222 <param name="reference_database_version" value="2.0" />
223 </conditional>
224 </repeat>
225 </section>
226 <param name="log" value="true"/>
227 <output name="logfile" value="abricate/abricate_logfile.txt" lines_diff="1"/>
228 <output_collection name="output_json" type="list">
229 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
230 </output_collection>
231 </test>
232 <test expect_num_outputs="1"> <!-- TEST_2 bakta all files -->
233 <section name="tool_section">
234 <repeat name="tools">
235 <conditional name="select_tool">
236 <param name="tool_list" value="bakta"/>
237 <param name="input" value="bakta/bakta.json" ftype="json"/>
238 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
239 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide.fasta" ftype="fasta"/>
240 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
241 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
242 <param name="reference_database_version" value="1.6.1"/>
243 </conditional>
244 </repeat>
245 </section>
246 <output_collection name="output_json" type="list" count="1">
247 <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
248 </output_collection>
249 </test>
250 <test expect_num_outputs="1"> <!-- TEST_3 All tool in repeat -->
251 <section name="tool_section">
252 <repeat name="tools">
253 <conditional name="select_tool">
254 <param name="tool_list" value="abricate"/>
255 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
256 <param name="analysis_software_version" value="1.0"/>
257 <param name="reference_database_version" value="2.0" />
258 </conditional>
259 </repeat>
260 <repeat name="tools">
261 <conditional name="select_tool">
262 <param name="tool_list" value="bakta"/>
263 <param name="input" value="bakta/bakta.json" ftype="json"/>
264 </conditional>
265 </repeat>
266 <repeat name="tools">
267 <conditional name="select_tool">
268 <param name="tool_list" value="bandage"/>
269 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
270 </conditional>
271 </repeat>
272 <repeat name="tools">
273 <conditional name="select_tool">
274 <param name="tool_list" value="bracken"/>
275 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
276 <param name="bracken/bracken_kraken_report" ftype="tabular" />
277 <param name="threshold" value="0" />
278 <param name="read_length" value="100"/>
279 <param name="level" value="S"/>
280 </conditional>
281 </repeat>
282 <repeat name="tools">
283 <conditional name="select_tool">
284 <param name="tool_list" value="fastp"/>
285 <param name="input" value="fastp/fastp_report.json" ftype="json"/>
286 </conditional>
287 </repeat>
288 <repeat name="tools">
289 <conditional name="select_tool">
290 <param name="tool_list" value="integronfinder2"/>
291 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
292 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
293 </conditional>
294 </repeat>
295 <repeat name="tools">
296 <conditional name="select_tool">
297 <param name="tool_list" value="isescan"/>
298 <param name="input" value="isescan/results.tsv" ftype="tabular"/>
299 <param name="orf_fna_file" value="isescan/orf.fna" ftype="fasta"/>
300 <param name="orf_faa_file" value="isescan/orf.faa" ftype="fasta"/>
301 <param name="is_fna_file" value="isescan/is.fna" ftype="fasta"/>
302 </conditional>
303 </repeat>
304 <repeat name="tools">
305 <conditional name="select_tool">
306 <param name="tool_list" value="kraken2"/>
307 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
308 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
309 </conditional>
310 </repeat>
311 <repeat name="tools">
312 <conditional name="select_tool">
313 <param name="tool_list" value="plasmidfinder"/>
314 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
315 <param name="genome_hit_file_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
316 <param name="plasmid_sequence_file_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
317 </conditional>
318 </repeat>
319 <repeat name="tools">
320 <conditional name="select_tool">
321 <param name="tool_list" value="quast"/>
322 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
323 </conditional>
324 </repeat>
325 <repeat name="tools">
326 <conditional name="select_tool">
327 <param name="tool_list" value="recentrifuge"/>
328 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
329 <param name="rcf_stat_file_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
330 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
331 </conditional>
332 </repeat>
333 <repeat name="tools">
334 <conditional name="select_tool">
335 <param name="tool_list" value="refseqmasher"/>
336 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
337 </conditional>
338 </repeat>
339 <repeat name="tools">
340 <conditional name="select_tool">
341 <param name="tool_list" value="shovill"/>
342 <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
343 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
344 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
345 </conditional>
346 </repeat>
347 <repeat name="tools">
348 <conditional name="select_tool">
349 <param name="tool_list" value="staramr"/>
350 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
351 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
352 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
353 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
354 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
355 </conditional>
356 </repeat>
357 <repeat name="tools">
358 <conditional name="select_tool">
359 <param name="tool_list" value="tabular_file"/>
360 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
361 </conditional>
362 </repeat>
363 </section>
364 <output_collection name="output_json" type="list" count="15">
365 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
366 <expand macro="element_assert" name="bakta_1_output" text="UniRef50_A0A0H2ZNL3"/>
367 <expand macro="element_assert" name="bandage_2_output" text="3042326"/>
368 <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/>
369 <expand macro="element_assert" name="fastp_4_output" text="705053822"/>
370 <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/>
371 <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/>
372 <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis_ATCC_29212"/>
373 <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/>
374 <expand macro="element_assert" name="quast_9_output" text="2944723"/>
375 <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/>
376 <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/>
377 <expand macro="element_assert" name="shovill_12_output" text="436224"/>
378 <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/>
379 <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/>
380 </output_collection>
381 </test>
382 <test expect_num_outputs="2"> <!-- TEST_4 repeat with summary option -->
383 <section name="tool_section">
384 <repeat name="tools">
385 <conditional name="select_tool">
386 <param name="tool_list" value="abricate"/>
387 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
388 <param name="analysis_software_version" value="1.0"/>
389 <param name="reference_database_version" value="2.0" />
390 </conditional>
391 </repeat>
392 <repeat name="tools">
393 <conditional name="select_tool">
394 <param name="tool_list" value="bakta"/>
395 <param name="input" value="bakta/bakta.json" ftype="json"/>
396 </conditional>
397 </repeat>
398 <repeat name="tools">
399 <conditional name="select_tool">
400 <param name="tool_list" value="bandage"/>
401 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
402 </conditional>
403 </repeat>
404 <repeat name="tools">
405 <conditional name="select_tool">
406 <param name="tool_list" value="bracken"/>
407 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
408 <param name="bracken/bracken_kraken_report" ftype="tabular" />
409 <param name="threshold" value="0" />
410 <param name="read_length" value="100"/>
411 <param name="level" value="S"/>
412 </conditional>
413 </repeat>
414 <repeat name="tools">
415 <conditional name="select_tool">
416 <param name="tool_list" value="fastp"/>
417 <param name="input" value="fastp/fastp_report.json" ftype="json"/>
418 </conditional>
419 </repeat>
420 <repeat name="tools">
421 <conditional name="select_tool">
422 <param name="tool_list" value="integronfinder2"/>
423 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
424 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
425 </conditional>
426 </repeat>
427 <repeat name="tools">
428 <conditional name="select_tool">
429 <param name="tool_list" value="isescan"/>
430 <param name="input" value="isescan/results.tsv" ftype="tabular"/>
431 <param name="orf_fna_file" value="isescan/orf.fna" ftype="fasta"/>
432 <param name="orf_faa_file" value="isescan/orf.faa" ftype="fasta"/>
433 <param name="is_fna_file" value="isescan/is.fna" ftype="fasta"/>
434 </conditional>
435 </repeat>
436 <repeat name="tools">
437 <conditional name="select_tool">
438 <param name="tool_list" value="kraken2"/>
439 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
440 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
441 </conditional>
442 </repeat>
443 <repeat name="tools">
444 <conditional name="select_tool">
445 <param name="tool_list" value="plasmidfinder"/>
446 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
447 <param name="genome_hit_file_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
448 <param name="plasmid_sequence_file_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
449 </conditional>
450 </repeat>
451 <repeat name="tools">
452 <conditional name="select_tool">
453 <param name="tool_list" value="quast"/>
454 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
455 </conditional>
456 </repeat>
457 <repeat name="tools">
458 <conditional name="select_tool">
459 <param name="tool_list" value="recentrifuge"/>
460 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
461 <param name="rcf_stat_file_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
462 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
463 </conditional>
464 </repeat>
465 <repeat name="tools">
466 <conditional name="select_tool">
467 <param name="tool_list" value="refseqmasher"/>
468 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
469 </conditional>
470 </repeat>
471 <repeat name="tools">
472 <conditional name="select_tool">
473 <param name="tool_list" value="shovill"/>
474 <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
475 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
476 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
477 </conditional>
478 </repeat>
479 <repeat name="tools">
480 <conditional name="select_tool">
481 <param name="tool_list" value="staramr"/>
482 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
483 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
484 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
485 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
486 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
487 </conditional>
488 </repeat>
489 <repeat name="tools">
490 <conditional name="select_tool">
491 <param name="tool_list" value="tabular_file"/>
492 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
493 </conditional>
494 </repeat>
495 </section>
496 <param name="summarize" value="true"/>
497 <output name="summary_json" value="summarize/summarize.json" lines_diff="6"/>
498 </test>
499 </tests>
500 <help><![CDATA[**What it does**
501 efljvl
502 zvlzhv
503 ]]></help>
504 <expand macro="citations"/>
505 </tool>